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Yorodumi- PDB-8j60: Structural and mechanistic insight into ribosomal ITS2 RNA proces... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8j60 | ||||||
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Title | Structural and mechanistic insight into ribosomal ITS2 RNA processing by nuclease-kinase machinery | ||||||
Components |
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Keywords | RNA BINDING PROTEIN / endoribonuclease / ribosome biosynthesis / Las1 / Grc3 | ||||||
Function / homology | Function and homology information polynucleotide 5'-hydroxyl-kinase activity / Las1 complex / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, large subunit precursor / maturation of LSU-rRNA / endonuclease activity / ATP binding / nucleus Similarity search - Function | ||||||
Biological species | Cyberlindnera jadinii (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å | ||||||
Authors | Chen, J. / Chen, H. / Li, S. / Lin, X. / Hu, R. / Zhang, K. / Liu, L. | ||||||
Funding support | China, 1items
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Citation | Journal: Elife / Year: 2024 Title: Structural and mechanistic insights into ribosomal ITS2 RNA processing by nuclease-kinase machinery. Authors: Jiyun Chen / Hong Chen / Shanshan Li / Xiaofeng Lin / Rong Hu / Kaiming Zhang / Liang Liu / Abstract: Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a ...Precursor ribosomal RNA (pre-rRNA) processing is a key step in ribosome biosynthesis and involves numerous RNases. A HEPN (higher eukaryote and prokaryote nucleotide binding) nuclease Las1 and a polynucleotide kinase Grc3 assemble into a tetramerase responsible for rRNA maturation. Here, we report the structures of full-length and Las1-Grc3 complexes, and Las1. The Las1-Grc3 structures show that the central coiled-coil domain of Las1 facilitates pre-rRNA binding and cleavage, while the Grc3 C-terminal loop motif directly binds to the HEPN active center of Las1 and regulates pre-rRNA cleavage. Structural comparison between Las1 and Las1-Grc3 complex exhibits that Grc3 binding induces conformational rearrangements of catalytic residues associated with HEPN nuclease activation. Biochemical assays identify that Las1 processes pre-rRNA at the two specific sites (C2 and C2'), which greatly facilitates rRNA maturation. Our structures and specific pre-rRNA cleavage findings provide crucial insights into the mechanism and pathway of pre-rRNA processing in ribosome biosynthesis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8j60.cif.gz | 241.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8j60.ent.gz | 182.2 KB | Display | PDB format |
PDBx/mmJSON format | 8j60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8j60_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8j60_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8j60_validation.xml.gz | 48.8 KB | Display | |
Data in CIF | 8j60_validation.cif.gz | 71.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j6/8j60 ftp://data.pdbj.org/pub/pdb/validation_reports/j6/8j60 | HTTPS FTP |
-Related structure data
Related structure data | 33735MC 7y16C 7y17C 7y18C 8j5yC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 69612.867 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyberlindnera jadinii (fungus) / Gene: GRC3, BN1211_2636, CYBJADRAFT_171070 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H5C3P3 #2: Protein | Mass: 49413.621 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyberlindnera jadinii (fungus) / Gene: LAS1, BN1211_1791 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A0H5CBH3 Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: CjLas1-Grc3 complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Source (natural) | Organism: Cyberlindnera jadinii (fungus) |
Source (recombinant) | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 523843 / Symmetry type: POINT | ||||||||||||||||||||||||
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